Photoregulating RNA Digestion Using Azobenzene Linked Dumbbell Antisense Oligodeoxynucleotides

Introduction of 4,4′-bis­(hydroxymethyl)-azobenzene (azo) to dumbbell hairpin oligonucleotides at the loop position was able to reversibly control the stability of the whole hairpin structure via UV or visible light irradiation. Here, we designed and synthesized a series of azobenzene linked dumbbell antisense oligodeoxynucleotides (asODNs) containing two terminal hairpins that are composed of an asODN and a short inhibitory sense strand. Thermal melting studies of these azobenzene linked dumbbell asODNs indicated that efficient <i>trans</i> to <i>cis</i> photoisomerization of azobenzene moieties induced large difference in thermal stability (Δ<i>T</i>_m = 12.1–21.3 °C). In addition, photomodulation of their RNA binding abilities and RNA digestion by RNase H was investigated. The <i>trans</i>-azobenzene linked asODNs with the optimized base pairs between asODN strands and inhibitory sense strands could only bind few percentage of the target RNA, while it was able to recover their binding to the target RNA and degrade it by RNase H after light irradiation. Upon optimization, it is promising to use these azobenzene linked asODNs for reversible spatial and temporal regulation of antisense activities based on both steric binding and RNA digestion by RNase H

Mirror-Image Thymidine Discriminates against Incorporation of Deoxyribonucleotide Triphosphate into DNA and Repairs Itself by DNA Polymerases

DNA polymerases are known to recognize preferably d-nucleotides over l-nucleotides during DNA synthesis. Here, we report that several general DNA polymerases catalyze polymerization reactions of nucleotides directed by the DNA template containing an l-thymidine (l-T). The results display that the 5′–3′ primer extension of natural nucleotides get to the end at chiral modification site with Taq and Phanta Max DNA polymerases, but the primer extension proceeds to the end of the template catalyzed by Deep Vent (exo^–), Vent (exo^–), and Therminator DNA polymerases. Furthermore, templating l-nucleoside displays a lag in the deoxyribonucleotide triphosphate (dNTP) incorporation rates relative to natural template by kinetics analysis, and polymerase chain reactions were inhibited with the DNA template containing two or three consecutive l-Ts. Most interestingly, no single base mutation or mismatch mixture corresponding to the location of l-T in the template was found, which is physiologically significant because they provide a theoretical basis on the involvement of DNA polymerase in the effective repair of l-T that may lead to cytotoxicity

Role of Secondary Particle Formation in the Persistence of Silver Nanoparticles in Humic Acid Containing Water under Light Irradiation

The wide use of silver nanoparticles (AgNPs) leads to the increasing release of AgNPs into the environment. Dissolved organic matter (DOM) is a key factor affecting the behaviors and fate of AgNPs in the aquatic environment. However, the mechanisms for the DOM-mediated transformations of AgNPs are still not fully understood. In this study, we investigated the persistence of AgNPs in the aquatic environment in the presence of different concentrations of humic acid (HA) over periods of time up to 14 days. The Ag species were monitored and characterized by absorption spectrometry, transmission electron microscopy (TEM), inductively coupled plasma mass spectrometry (ICP-MS), and multicollector ICP-MS (MC-ICP-MS). Results showed that the long-term persistence of AgNPs in HA-containing water was determined by two critical concentrations of HA. When the HA concentration exceeded a lower critical value, AgNPs could be persistent in the solution, and a large number of AgNPs were formed secondarily from the HA-induced reduction of the Ag⁺ ions released from the primary AgNPs, causing a redistribution of the particle size. With the HA concentration above a higher critical value, AgNPs could persist in the solution without a significant change in particle size. Notably, we used Ag isotope fractionation to investigate the transformation mechanism of AgNPs. The natural isotopic analysis by MC-ICP-MS revealed that the size redistribution of AgNPs caused significant Ag isotope fractionation, which gave additional evidence for the proposed mechanisms. This study provides new insights into the environmental fate of engineered AgNPs and highlights the usefulness of stable isotope fractionation in environmental nanotechnology

Antibody-Free Colorimetric Detection of Total Aflatoxins in Rice Based on a Simple Two-Step Chromogenic Reaction

The prevalently used immunoassays for fast screening of aftatoxins (AFs) usually cannot meet the requirement for simultaneous determination of total AFs (aflatoxin B₁ + aflatoxin B₂ + aflatoxin G₁ + aflatoxin G₂) due to the deficiency of highly group-specific antibodies. This paper describes a two-step chromogenic reaction based method to quantitatively detect total AFs in rice using colorimetric measurement without antibody. In the method, colorless AFs transform into green-colored indophenol products through the reaction with sodium hydroxide and 2,6-dibromoquinone-4-chloroimide (DBQC) successively, allowing selectively determining total AFs up to 3.9 μg/kg over other competitive mycotoxins under optimal conditions by a UV–vis spectrophotometer. In addition, the colorimetric measurement results of the rice samples agree well with that of a standard HPLC method, demonstrating the good reliability and applicability of the method. Uniquely, the method has potential for on-site detection of total AFs in rice when using a nylon membrane-based device